Report generated on 27-May-2022 at 09:08:27 by pytest-html v3.1.1
-| Packages | -{"pluggy": "1.0.0", "py": "1.11.0", "pytest": "6.2.5"} |
| Platform | -Linux-5.13.0-44-generic-x86_64-with-glibc2.29 |
| Plugins | -{"anyio": "3.5.0", "asyncio": "0.17.2", "celery": "0.0.0", "cov": "3.0.0", "html": "3.1.1", "json-report": "1.4.1", "metadata": "1.11.0", "mock": "3.7.0", "postgresql": "4.1.0", "pythonpath": "0.7.3", "shard": "0.1.2"} |
| Python | -3.8.10 |
5 tests ran in 162.57 seconds.
-(Un)check the boxes to filter the results.
3 passed, 0 skipped, 2 failed, 0 errors, 0 expected failures, 0 unexpected passes -| Result | -Test | -Duration | -Links |
|---|---|---|---|
| No results found. Try to check the filters | |||
| Failed | -test/functional/test_toolbox_pytest.py::test_tool[testtoolshed.g2.bx.psu.edu/repos/agpetit/estimate_cut_sub_trajectories/estimate_cut_sub_trajectories/0.1.0_test_2] | -38.80 | -|
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- testcases = ('testtoolshed.g2.bx.psu.edu/repos/agpetit/estimate_cut_sub_trajectories/estimate_cut_sub_trajectories/0.1.0_test_2', ...d.g2.bx.psu.edu/repos/agpetit/estimate_cut_sub_trajectories/estimate_cut_sub_trajectories/0.1.0 testMethod=runTest>, 1) driver = <functional.test_toolbox_pytest.DefaultGalaxyTestDriver object at 0x7f227250c280> @pytest.mark.parametrize("testcases", cases(), ids=idfn) def test_tool(testcases, driver): test = testcases[1] > test.do_it(test_index=testcases[2]) test/functional/test_toolbox_pytest.py:84: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/functional/test_toolbox.py:35: in do_it verify_tool(tool_id, self.galaxy_interactor, resource_parameters=resource_parameters, test_index=test_index, tool_version=tool_version, register_job_data=register_job_data) lib/galaxy/tool_util/verify/interactor.py:1127: in verify_tool raise e lib/galaxy/tool_util/verify/interactor.py:1123: in verify_tool job_stdio = _verify_outputs(testdef, test_history, jobs, data_list, data_collection_list, galaxy_interactor, quiet=quiet) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ testdef = <galaxy.tool_util.verify.interactor.ToolTestDescription object at 0x7f226f4f3c40>, history = '54f2a3a23292eb07' jobs = [{'create_time': '2022-05-27T07:07:09.529613', 'exit_code': None, 'galaxy_version': '22.01', 'history_id': '54f2a3a23292eb07', ...}] data_list = {'cut_log': {'create_time': '2022-05-27T07:07:09.533075', 'data_type': 'galaxy.datatypes.data.Text', 'deleted': False,...157069a5-6727-4eb8-9d80-8a551afe1093', 'validated_state': 'unknown', 'validated_state_message': None, 'visible': True}} data_collection_list = {'output_traj': {'collection_type': 'list', 'contents_url': '/api/dataset_collections/5729865256bc2525/contents/5729865256bc2525', 'create_time': '2022-05-27T07:07:09.531693', 'deleted': False, ...}} galaxy_interactor = <galaxy.tool_util.verify.interactor.GalaxyInteractorApi object at 0x7f2214721b50>, quiet = False def _verify_outputs(testdef, history, jobs, data_list, data_collection_list, galaxy_interactor, quiet=False): assert len(jobs) == 1, "Test framework logic error, somehow tool test resulted in more than one job." job = jobs[0] found_exceptions = [] def register_exception(e): if not found_exceptions and not quiet: # Only print this stuff out once. for stream in ['stdout', 'stderr']: if stream in job_stdio: print(_format_stream(job_stdio[stream], stream=stream, format=True), file=sys.stderr) found_exceptions.append(e) if testdef.expect_failure: if testdef.outputs: raise Exception("Cannot specify outputs in a test expecting failure.") maxseconds = testdef.maxseconds # Wait for the job to complete and register expections if the final # status was not what test was expecting. job_failed = False try: galaxy_interactor.wait_for_job(job['id'], history, maxseconds) except Exception as e: job_failed = True if not testdef.expect_failure: found_exceptions.append(e) job_stdio = galaxy_interactor.get_job_stdio(job['id']) if testdef.num_outputs is not None: expected = testdef.num_outputs actual = len(data_list) + len(data_collection_list) if expected != actual: message = f"Incorrect number of outputs - expected {expected}, found {actual}: datasets {data_list.keys()} collections {data_collection_list.keys()}" error = AssertionError(message) register_exception(error) if not job_failed and testdef.expect_failure: error = AssertionError("Expected job to fail but Galaxy indicated the job successfully completed.") register_exception(error) expect_exit_code = testdef.expect_exit_code if expect_exit_code is not None: exit_code = job_stdio["exit_code"] if str(expect_exit_code) != str(exit_code): error = AssertionError(f"Expected job to complete with exit code {expect_exit_code}, found {exit_code}") register_exception(error) for output_index, output_dict in enumerate(testdef.outputs): # Get the correct hid name = output_dict["name"] outfile = output_dict["value"] attributes = output_dict["attributes"] output_testdef = Bunch(name=name, outfile=outfile, attributes=attributes) try: output_data = data_list[name] except (TypeError, KeyError): # Legacy - fall back on ordered data list access if data_list is # just a list (case with twill variant or if output changes its # name). if hasattr(data_list, "values"): output_data = list(data_list.values())[output_index] else: output_data = data_list[len(data_list) - len(testdef.outputs) + output_index] assert output_data is not None try: galaxy_interactor.verify_output(history, jobs, output_data, output_testdef=output_testdef, tool_id=job['tool_id'], maxseconds=maxseconds, tool_version=testdef.tool_version) except Exception as e: register_exception(e) other_checks = { "command_line": "Command produced by the job", "command_version": "Tool version indicated during job execution", "stdout": "Standard output of the job", "stderr": "Standard error of the job", } # TODO: Only hack the stdio like this for older profile, for newer tool profiles # add some syntax for asserting job messages maybe - or just drop this because exit # code and regex on stdio can be tested directly - so this is really testing Galaxy # core handling more than the tool. job_messages = job_stdio.get("job_messages") or [] stdout_prefix = "" stderr_prefix = "" for job_message in job_messages: message_type = job_message.get("type") if message_type == "regex" and job_message.get("stream") == "stderr": stderr_prefix += f"{job_message.get('desc') or ''}\n" elif message_type == "regex" and job_message.get("stream") == "stdout": stdout_prefix += f"{job_message.get('desc') or ''}\n" elif message_type == "exit_code": stderr_prefix += f"{job_message.get('desc') or ''}\n" else: raise Exception(f"Unknown job message type [{message_type}] in [{job_message}]") for what, description in other_checks.items(): if getattr(testdef, what, None) is not None: try: raw_data = job_stdio[what] assertions = getattr(testdef, what) if what == "stdout": data = stdout_prefix + raw_data elif what == "stderr": data = stderr_prefix + raw_data else: data = raw_data verify_assertions(data, assertions) except AssertionError as err: errmsg = f'{description} different than expected\n' errmsg += util.unicodify(err) register_exception(AssertionError(errmsg)) for output_collection_def in testdef.output_collections: try: name = output_collection_def.name # TODO: data_collection_list is clearly a bad name for dictionary. if name not in data_collection_list: message = f"Failed to find output [{name}], tool outputs include [{','.join(data_collection_list.keys())}]" raise AssertionError(message) # Data collection returned from submission, elements may have been populated after # the job completed so re-hit the API for more information. data_collection_id = data_collection_list[name]["id"] galaxy_interactor.verify_output_collection(output_collection_def, data_collection_id, history, job['tool_id']) except Exception as e: register_exception(e) if found_exceptions and not testdef.expect_test_failure: > raise JobOutputsError(found_exceptions, job_stdio) E galaxy.tool_util.verify.interactor.JobOutputsError: Output cut_log: different than expected E Expected 241+-0 lines in the output found 163 lib/galaxy/tool_util/verify/interactor.py:1299: JobOutputsError ------------------------------Captured stderr call------------------------------ 2022-05-27 09:06:44,120 DEBUG [multipart.multipart] Calling on_field_start with no data -2022-05-27 09:06:44,121 DEBUG [multipart.multipart] Calling on_field_name with data[0:4] -2022-05-27 09:06:44,121 DEBUG [multipart.multipart] Calling on_field_data with data[5:153] -2022-05-27 09:06:44,121 DEBUG [multipart.multipart] Calling on_field_end with no data -2022-05-27 09:06:44,121 DEBUG [multipart.multipart] Calling on_end with no data -2022-05-27 09:06:45,213 INFO [galaxy.tools] Validated and populated state for tool request (21.598 ms) -2022-05-27 09:06:45,219 DEBUG [galaxy.tools.actions.upload] Persisted uploads (0.142 ms) -2022-05-27 09:06:45,353 DEBUG [galaxy.tools.actions.upload] Checked uploads (134.155 ms) -2022-05-27 09:06:45,360 DEBUG [galaxy.tools.actions.upload] Created upload job (6.274 ms) -2022-05-27 09:06:45,381 INFO [galaxy.web_stack.handlers] (Job[id=7,tool_id=upload1]) Handler '_default_' assigned using 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method -2022-05-27 09:06:46,309 INFO [galaxy.jobs.handler] (7) Job dispatched -2022-05-27 09:06:46,485 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmptoruqmiy/job_working_directory/000/7/tool_script.sh] for tool command [python '/tmp/tmptoruqmiy/galaxy-dev/tools/data_source/upload.py' '/tmp/tmptoruqmiy/galaxy-dev' '/tmp/tmptoruqmiy/job_working_directory/000/7/registry.xml' '/tmp/upload_params_n9cdh_8t' '8:/tmp/tmptoruqmiy/job_working_directory/000/7/working/dataset_af8d1b0c-d748-4b88-935e-429302b926ec_files:/tmp/tmptoruqmiy/files/a/f/8/dataset_af8d1b0c-d748-4b88-935e-429302b926ec.dat'] -2022-05-27 09:06:54,095 INFO [galaxy.tools] Validated and populated state for tool request (24.710 ms) -2022-05-27 09:06:54,102 DEBUG [galaxy.tools.actions.upload] Persisted uploads (0.144 ms) -2022-05-27 09:06:54,215 DEBUG [galaxy.tools.actions.upload] Checked uploads (113.287 ms) -2022-05-27 09:06:54,221 DEBUG [galaxy.tools.actions.upload] Created upload job (5.835 ms) -2022-05-27 09:06:54,242 INFO [galaxy.web_stack.handlers] (Job[id=8,tool_id=upload1]) Handler '_default_' assigned using 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method -2022-05-27 09:06:54,873 INFO [galaxy.jobs.handler] (8) Job dispatched -2022-05-27 09:06:55,123 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmptoruqmiy/job_working_directory/000/8/tool_script.sh] for tool command [python '/tmp/tmptoruqmiy/galaxy-dev/tools/data_source/upload.py' '/tmp/tmptoruqmiy/galaxy-dev' '/tmp/tmptoruqmiy/job_working_directory/000/8/registry.xml' '/tmp/upload_params__n8zpgmo' '9:/tmp/tmptoruqmiy/job_working_directory/000/8/working/dataset_2f2d7be8-929e-4b65-a898-06a921300c73_files:/tmp/tmptoruqmiy/files/2/f/2/dataset_2f2d7be8-929e-4b65-a898-06a921300c73.dat'] -2022-05-27 09:07:01,790 INFO [galaxy.tools] Validated and populated state for tool request (23.541 ms) -2022-05-27 09:07:01,796 DEBUG [galaxy.tools.actions.upload] Persisted uploads (0.142 ms) -2022-05-27 09:07:01,908 DEBUG [galaxy.tools.actions.upload] Checked uploads (112.494 ms) -2022-05-27 09:07:01,916 DEBUG [galaxy.tools.actions.upload] Created upload job (7.217 ms) -2022-05-27 09:07:01,941 INFO [galaxy.web_stack.handlers] (Job[id=9,tool_id=upload1]) Handler '_default_' assigned using 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method -2022-05-27 09:07:02,320 INFO [galaxy.jobs.handler] (9) Job dispatched -2022-05-27 09:07:02,533 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmptoruqmiy/job_working_directory/000/9/tool_script.sh] for tool command [python '/tmp/tmptoruqmiy/galaxy-dev/tools/data_source/upload.py' '/tmp/tmptoruqmiy/galaxy-dev' '/tmp/tmptoruqmiy/job_working_directory/000/9/registry.xml' '/tmp/upload_params_d9ksd_uu' '10:/tmp/tmptoruqmiy/job_working_directory/000/9/working/dataset_1cbe15a0-33cd-4c77-a7eb-cfce8034f2bb_files:/tmp/tmptoruqmiy/files/1/c/b/dataset_1cbe15a0-33cd-4c77-a7eb-cfce8034f2bb.dat'] -2022-05-27 09:07:09,478 INFO [galaxy.tools] Validated and populated state for tool request (23.189 ms) -2022-05-27 09:07:09,492 INFO [galaxy.tools.actions] Handled collection output named output_traj for tool testtoolshed.g2.bx.psu.edu/repos/agpetit/estimate_cut_sub_trajectories/estimate_cut_sub_trajectories/0.1.0 (2.367 ms) -2022-05-27 09:07:09,494 INFO [galaxy.tools.actions] Handled output named cut_log for tool testtoolshed.g2.bx.psu.edu/repos/agpetit/estimate_cut_sub_trajectories/estimate_cut_sub_trajectories/0.1.0 (1.967 ms) -2022-05-27 09:07:09,511 INFO [galaxy.tools.actions] Added output datasets to history (17.096 ms) -2022-05-27 09:07:09,515 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=testtoolshed.g2.bx.psu.edu/repos/agpetit/estimate_cut_sub_trajectories/estimate_cut_sub_trajectories/0.1.0] complete, ready to be enqueued (3.762 ms) -2022-05-27 09:07:09,558 INFO [galaxy.web_stack.handlers] (Job[id=10,tool_id=testtoolshed.g2.bx.psu.edu/repos/agpetit/estimate_cut_sub_trajectories/estimate_cut_sub_trajectories/0.1.0]) Handler '_default_' assigned using 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method -2022-05-27 09:07:09,901 INFO [galaxy.jobs.handler] (10) Job dispatched -2022-05-27 09:07:10,139 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmptoruqmiy/job_working_directory/000/10/tool_script.sh] for tool command [[ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/aepetit/miniconda3/bin/activate' '/home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/aepetit/miniconda3/bin/activate' '/home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/aepetit/miniconda3/bin/activate' '/home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; ln -s '/tmp/tmptoruqmiy/files/a/f/8/dataset_af8d1b0c-d748-4b88-935e-429302b926ec.dat' 'PIP2.1_test.gro' && ln -s '/tmp/tmptoruqmiy/files/2/f/2/dataset_2f2d7be8-929e-4b65-a898-06a921300c73.dat' 'PIP2.1_test.xtc' && ln -s '/tmp/tmptoruqmiy/files/1/c/b/dataset_1cbe15a0-33cd-4c77-a7eb-cfce8034f2bb.dat' 'estimated_number_of_sub_trajectories.tsv' && python '/tmp/tmptoruqmiy/shed_tools/testtoolshed.g2.bx.psu.edu/repos/agpetit/estimate_cut_sub_trajectories/c09cf8acc4de/estimate_cut_sub_trajectories/estimate_cut_sub_trajectories.py' --verbose --gro_file 'PIP2.1_test.gro' --xtc_file 'PIP2.1_test.xtc' --log_output 'log/cut_trajectories.log' --output_directory 'out/' --nbr_sub_traj 'estimated_number_of_sub_trajectories.tsv' --group_output 0 --number_cpus "${GALAXY_SLOTS:-1}"] ----------------------- >> begin tool stdout << ----------------------- - ------------------------ >> end tool stdout << ------------------------ - ----------------------- >> begin tool stderr << ----------------------- - ------------------------ >> end tool stderr << ------------------------ - - -------------------------------Captured log call-------------------------------- DEBUG multipart.multipart:multipart.py:604 Calling on_field_start with no data -DEBUG multipart.multipart:multipart.py:601 Calling on_field_name with data[0:4] -DEBUG multipart.multipart:multipart.py:601 Calling on_field_data with data[5:153] -DEBUG multipart.multipart:multipart.py:604 Calling on_field_end with no data -DEBUG multipart.multipart:multipart.py:604 Calling on_end with no data | |||
| Failed | -test/functional/test_toolbox_pytest.py::test_tool[testtoolshed.g2.bx.psu.edu/repos/agpetit/estimate_cut_sub_trajectories/estimate_cut_sub_trajectories/0.1.0_test_3] | -40.43 | -|
|
- testcases = ('testtoolshed.g2.bx.psu.edu/repos/agpetit/estimate_cut_sub_trajectories/estimate_cut_sub_trajectories/0.1.0_test_3', ...d.g2.bx.psu.edu/repos/agpetit/estimate_cut_sub_trajectories/estimate_cut_sub_trajectories/0.1.0 testMethod=runTest>, 2) driver = <functional.test_toolbox_pytest.DefaultGalaxyTestDriver object at 0x7f227250c280> @pytest.mark.parametrize("testcases", cases(), ids=idfn) def test_tool(testcases, driver): test = testcases[1] > test.do_it(test_index=testcases[2]) test/functional/test_toolbox_pytest.py:84: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/functional/test_toolbox.py:35: in do_it verify_tool(tool_id, self.galaxy_interactor, resource_parameters=resource_parameters, test_index=test_index, tool_version=tool_version, register_job_data=register_job_data) lib/galaxy/tool_util/verify/interactor.py:1127: in verify_tool raise e lib/galaxy/tool_util/verify/interactor.py:1123: in verify_tool job_stdio = _verify_outputs(testdef, test_history, jobs, data_list, data_collection_list, galaxy_interactor, quiet=quiet) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ testdef = <galaxy.tool_util.verify.interactor.ToolTestDescription object at 0x7f226f22bd30>, history = '8155e4b4bf1581ff' jobs = [{'create_time': '2022-05-27T07:07:50.059003', 'exit_code': None, 'galaxy_version': '22.01', 'history_id': '8155e4b4bf1581ff', ...}] data_list = {'cut_log': {'create_time': '2022-05-27T07:07:50.063180', 'data_type': 'galaxy.datatypes.data.Text', 'deleted': False,...11db857f-5e9e-40b7-ab71-3aba6213bc8b', 'validated_state': 'unknown', 'validated_state_message': None, 'visible': True}} data_collection_list = {'output_traj': {'collection_type': 'list', 'contents_url': '/api/dataset_collections/54f2a3a23292eb07/contents/54f2a3a23292eb07', 'create_time': '2022-05-27T07:07:50.061399', 'deleted': False, ...}} galaxy_interactor = <galaxy.tool_util.verify.interactor.GalaxyInteractorApi object at 0x7f2214721b50>, quiet = False def _verify_outputs(testdef, history, jobs, data_list, data_collection_list, galaxy_interactor, quiet=False): assert len(jobs) == 1, "Test framework logic error, somehow tool test resulted in more than one job." job = jobs[0] found_exceptions = [] def register_exception(e): if not found_exceptions and not quiet: # Only print this stuff out once. for stream in ['stdout', 'stderr']: if stream in job_stdio: print(_format_stream(job_stdio[stream], stream=stream, format=True), file=sys.stderr) found_exceptions.append(e) if testdef.expect_failure: if testdef.outputs: raise Exception("Cannot specify outputs in a test expecting failure.") maxseconds = testdef.maxseconds # Wait for the job to complete and register expections if the final # status was not what test was expecting. job_failed = False try: galaxy_interactor.wait_for_job(job['id'], history, maxseconds) except Exception as e: job_failed = True if not testdef.expect_failure: found_exceptions.append(e) job_stdio = galaxy_interactor.get_job_stdio(job['id']) if testdef.num_outputs is not None: expected = testdef.num_outputs actual = len(data_list) + len(data_collection_list) if expected != actual: message = f"Incorrect number of outputs - expected {expected}, found {actual}: datasets {data_list.keys()} collections {data_collection_list.keys()}" error = AssertionError(message) register_exception(error) if not job_failed and testdef.expect_failure: error = AssertionError("Expected job to fail but Galaxy indicated the job successfully completed.") register_exception(error) expect_exit_code = testdef.expect_exit_code if expect_exit_code is not None: exit_code = job_stdio["exit_code"] if str(expect_exit_code) != str(exit_code): error = AssertionError(f"Expected job to complete with exit code {expect_exit_code}, found {exit_code}") register_exception(error) for output_index, output_dict in enumerate(testdef.outputs): # Get the correct hid name = output_dict["name"] outfile = output_dict["value"] attributes = output_dict["attributes"] output_testdef = Bunch(name=name, outfile=outfile, attributes=attributes) try: output_data = data_list[name] except (TypeError, KeyError): # Legacy - fall back on ordered data list access if data_list is # just a list (case with twill variant or if output changes its # name). if hasattr(data_list, "values"): output_data = list(data_list.values())[output_index] else: output_data = data_list[len(data_list) - len(testdef.outputs) + output_index] assert output_data is not None try: galaxy_interactor.verify_output(history, jobs, output_data, output_testdef=output_testdef, tool_id=job['tool_id'], maxseconds=maxseconds, tool_version=testdef.tool_version) except Exception as e: register_exception(e) other_checks = { "command_line": "Command produced by the job", "command_version": "Tool version indicated during job execution", "stdout": "Standard output of the job", "stderr": "Standard error of the job", } # TODO: Only hack the stdio like this for older profile, for newer tool profiles # add some syntax for asserting job messages maybe - or just drop this because exit # code and regex on stdio can be tested directly - so this is really testing Galaxy # core handling more than the tool. job_messages = job_stdio.get("job_messages") or [] stdout_prefix = "" stderr_prefix = "" for job_message in job_messages: message_type = job_message.get("type") if message_type == "regex" and job_message.get("stream") == "stderr": stderr_prefix += f"{job_message.get('desc') or ''}\n" elif message_type == "regex" and job_message.get("stream") == "stdout": stdout_prefix += f"{job_message.get('desc') or ''}\n" elif message_type == "exit_code": stderr_prefix += f"{job_message.get('desc') or ''}\n" else: raise Exception(f"Unknown job message type [{message_type}] in [{job_message}]") for what, description in other_checks.items(): if getattr(testdef, what, None) is not None: try: raw_data = job_stdio[what] assertions = getattr(testdef, what) if what == "stdout": data = stdout_prefix + raw_data elif what == "stderr": data = stderr_prefix + raw_data else: data = raw_data verify_assertions(data, assertions) except AssertionError as err: errmsg = f'{description} different than expected\n' errmsg += util.unicodify(err) register_exception(AssertionError(errmsg)) for output_collection_def in testdef.output_collections: try: name = output_collection_def.name # TODO: data_collection_list is clearly a bad name for dictionary. if name not in data_collection_list: message = f"Failed to find output [{name}], tool outputs include [{','.join(data_collection_list.keys())}]" raise AssertionError(message) # Data collection returned from submission, elements may have been populated after # the job completed so re-hit the API for more information. data_collection_id = data_collection_list[name]["id"] galaxy_interactor.verify_output_collection(output_collection_def, data_collection_id, history, job['tool_id']) except Exception as e: register_exception(e) if found_exceptions and not testdef.expect_test_failure: > raise JobOutputsError(found_exceptions, job_stdio) E galaxy.tool_util.verify.interactor.JobOutputsError: Output cut_log: different than expected E Expected 239+-0 lines in the output found 161 lib/galaxy/tool_util/verify/interactor.py:1299: JobOutputsError ------------------------------Captured stderr call------------------------------ 2022-05-27 09:07:23,056 DEBUG [multipart.multipart] Calling on_field_start with no data -2022-05-27 09:07:23,056 DEBUG [multipart.multipart] Calling on_field_name with data[0:4] -2022-05-27 09:07:23,056 DEBUG [multipart.multipart] Calling on_field_data with data[5:153] -2022-05-27 09:07:23,056 DEBUG [multipart.multipart] Calling on_field_end with no data -2022-05-27 09:07:23,056 DEBUG [multipart.multipart] Calling on_end with no data -2022-05-27 09:07:24,155 INFO [galaxy.tools] Validated and populated state for tool request (22.557 ms) -2022-05-27 09:07:24,161 DEBUG [galaxy.tools.actions.upload] Persisted uploads (0.147 ms) -2022-05-27 09:07:24,267 DEBUG [galaxy.tools.actions.upload] Checked uploads (105.875 ms) -2022-05-27 09:07:24,273 DEBUG [galaxy.tools.actions.upload] Created upload job (6.109 ms) -2022-05-27 09:07:24,304 INFO [galaxy.web_stack.handlers] (Job[id=11,tool_id=upload1]) Handler '_default_' assigned using 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method -2022-05-27 09:07:24,687 INFO [galaxy.jobs.handler] (11) Job dispatched -2022-05-27 09:07:24,908 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmptoruqmiy/job_working_directory/000/11/tool_script.sh] for tool command [python '/tmp/tmptoruqmiy/galaxy-dev/tools/data_source/upload.py' '/tmp/tmptoruqmiy/galaxy-dev' '/tmp/tmptoruqmiy/job_working_directory/000/11/registry.xml' '/tmp/upload_params_149iajw4' '15:/tmp/tmptoruqmiy/job_working_directory/000/11/working/dataset_77bd9b6c-523e-47cf-9eab-81619349d30f_files:/tmp/tmptoruqmiy/files/7/7/b/dataset_77bd9b6c-523e-47cf-9eab-81619349d30f.dat'] -2022-05-27 09:07:32,387 INFO [galaxy.tools] Validated and populated state for tool request (22.918 ms) -2022-05-27 09:07:32,394 DEBUG [galaxy.tools.actions.upload] Persisted uploads (0.147 ms) -2022-05-27 09:07:32,506 DEBUG [galaxy.tools.actions.upload] Checked uploads (111.673 ms) -2022-05-27 09:07:32,512 DEBUG [galaxy.tools.actions.upload] Created upload job (6.064 ms) -2022-05-27 09:07:32,540 INFO [galaxy.web_stack.handlers] (Job[id=12,tool_id=upload1]) Handler '_default_' assigned using 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method -2022-05-27 09:07:33,244 INFO [galaxy.jobs.handler] (12) Job dispatched -2022-05-27 09:07:33,510 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmptoruqmiy/job_working_directory/000/12/tool_script.sh] for tool command [python '/tmp/tmptoruqmiy/galaxy-dev/tools/data_source/upload.py' '/tmp/tmptoruqmiy/galaxy-dev' '/tmp/tmptoruqmiy/job_working_directory/000/12/registry.xml' '/tmp/upload_params_t99uz5pr' '16:/tmp/tmptoruqmiy/job_working_directory/000/12/working/dataset_18454cb5-4d92-467e-a6fe-92717ffffe40_files:/tmp/tmptoruqmiy/files/1/8/4/dataset_18454cb5-4d92-467e-a6fe-92717ffffe40.dat'] -2022-05-27 09:07:40,449 INFO [galaxy.tools] Validated and populated state for tool request (22.896 ms) -2022-05-27 09:07:40,456 DEBUG [galaxy.tools.actions.upload] Persisted uploads (0.352 ms) -2022-05-27 09:07:40,576 DEBUG [galaxy.tools.actions.upload] Checked uploads (119.159 ms) -2022-05-27 09:07:40,584 DEBUG [galaxy.tools.actions.upload] Created upload job (8.363 ms) -2022-05-27 09:07:40,608 INFO [galaxy.web_stack.handlers] (Job[id=13,tool_id=upload1]) Handler '_default_' assigned using 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method -2022-05-27 09:07:40,935 INFO [galaxy.jobs.handler] (13) Job dispatched -2022-05-27 09:07:41,109 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmptoruqmiy/job_working_directory/000/13/tool_script.sh] for tool command [python '/tmp/tmptoruqmiy/galaxy-dev/tools/data_source/upload.py' '/tmp/tmptoruqmiy/galaxy-dev' '/tmp/tmptoruqmiy/job_working_directory/000/13/registry.xml' '/tmp/upload_params_e61k8ex6' '17:/tmp/tmptoruqmiy/job_working_directory/000/13/working/dataset_745f4487-3b81-44f5-9eb8-9d76e882a98a_files:/tmp/tmptoruqmiy/files/7/4/5/dataset_745f4487-3b81-44f5-9eb8-9d76e882a98a.dat'] -2022-05-27 09:07:50,014 INFO [galaxy.tools] Validated and populated state for tool request (24.877 ms) -2022-05-27 09:07:50,027 INFO [galaxy.tools.actions] Handled collection output named output_traj for tool testtoolshed.g2.bx.psu.edu/repos/agpetit/estimate_cut_sub_trajectories/estimate_cut_sub_trajectories/0.1.0 (0.776 ms) -2022-05-27 09:07:50,028 INFO [galaxy.tools.actions] Handled output named cut_log for tool testtoolshed.g2.bx.psu.edu/repos/agpetit/estimate_cut_sub_trajectories/estimate_cut_sub_trajectories/0.1.0 (0.902 ms) -2022-05-27 09:07:50,042 INFO [galaxy.tools.actions] Added output datasets to history (13.785 ms) -2022-05-27 09:07:50,045 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=testtoolshed.g2.bx.psu.edu/repos/agpetit/estimate_cut_sub_trajectories/estimate_cut_sub_trajectories/0.1.0] complete, ready to be enqueued (2.064 ms) -2022-05-27 09:07:50,082 INFO [galaxy.web_stack.handlers] (Job[id=14,tool_id=testtoolshed.g2.bx.psu.edu/repos/agpetit/estimate_cut_sub_trajectories/estimate_cut_sub_trajectories/0.1.0]) Handler '_default_' assigned using 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method -2022-05-27 09:07:50,482 INFO [galaxy.jobs.handler] (14) Job dispatched -2022-05-27 09:07:50,758 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmptoruqmiy/job_working_directory/000/14/tool_script.sh] for tool command [[ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/aepetit/miniconda3/bin/activate' '/home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/aepetit/miniconda3/bin/activate' '/home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/aepetit/miniconda3/bin/activate' '/home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; ln -s '/tmp/tmptoruqmiy/files/7/7/b/dataset_77bd9b6c-523e-47cf-9eab-81619349d30f.dat' 'PIP2.1_test.gro' && ln -s '/tmp/tmptoruqmiy/files/1/8/4/dataset_18454cb5-4d92-467e-a6fe-92717ffffe40.dat' 'PIP2.1_test.xtc' && ln -s '/tmp/tmptoruqmiy/files/7/4/5/dataset_745f4487-3b81-44f5-9eb8-9d76e882a98a.dat' 'PIP2.1_test_check.txt' && python '/tmp/tmptoruqmiy/shed_tools/testtoolshed.g2.bx.psu.edu/repos/agpetit/estimate_cut_sub_trajectories/c09cf8acc4de/estimate_cut_sub_trajectories/estimate_cut_sub_trajectories.py' --verbose --gro_file 'PIP2.1_test.gro' --xtc_file 'PIP2.1_test.xtc' --log_output 'log/cut_trajectories.log' --output_directory 'out/' --nbr_sub_traj '3' --input_check 'PIP2.1_test_check.txt' --start_traj '0' --end_traj '10' --group_output 0 --number_cpus "${GALAXY_SLOTS:-1}"] ----------------------- >> begin tool stdout << ----------------------- - ------------------------ >> end tool stdout << ------------------------ - ----------------------- >> begin tool stderr << ----------------------- - ------------------------ >> end tool stderr << ------------------------ - - -------------------------------Captured log call-------------------------------- DEBUG multipart.multipart:multipart.py:604 Calling on_field_start with no data -DEBUG multipart.multipart:multipart.py:601 Calling on_field_name with data[0:4] -DEBUG multipart.multipart:multipart.py:601 Calling on_field_data with data[5:153] -DEBUG multipart.multipart:multipart.py:604 Calling on_field_end with no data -DEBUG multipart.multipart:multipart.py:604 Calling on_end with no data | |||
| Passed | -test/functional/test_toolbox_pytest.py::test_tool[testtoolshed.g2.bx.psu.edu/repos/agpetit/concatenate_table/concatenate_table/1.0.0_test_1] | -30.08 | -|
|
- ------------------------------Captured stderr call------------------------------ 2022-05-27 09:05:57,130 DEBUG [multipart.multipart] Calling on_field_start with no data -2022-05-27 09:05:57,130 DEBUG [multipart.multipart] Calling on_field_name with data[0:4] -2022-05-27 09:05:57,131 DEBUG [multipart.multipart] Calling on_field_data with data[5:129] -2022-05-27 09:05:57,131 DEBUG [multipart.multipart] Calling on_field_end with no data -2022-05-27 09:05:57,131 DEBUG [multipart.multipart] Calling on_end with no data -2022-05-27 09:05:57,282 INFO [galaxy.managers.configuration] Galaxy extra version JSON file /tmp/tmptoruqmiy/galaxy-dev/version.json not loaded. -2022-05-27 09:05:57,369 INFO [galaxy.tools] Validated and populated state for tool request (23.134 ms) -2022-05-27 09:05:57,383 DEBUG [galaxy.tools.actions.upload] Persisted uploads (0.163 ms) -2022-05-27 09:05:57,525 DEBUG [galaxy.tools.actions.upload] Checked uploads (141.865 ms) -2022-05-27 09:05:57,531 DEBUG [galaxy.tools.actions.upload] Created upload job (5.830 ms) -2022-05-27 09:05:57,566 INFO [galaxy.web_stack.handlers] (Job[id=1,tool_id=upload1]) Handler '_default_' assigned using 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method -2022-05-27 09:05:58,195 INFO [galaxy.jobs.handler] (1) Job dispatched -2022-05-27 09:05:58,387 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmptoruqmiy/job_working_directory/000/1/tool_script.sh] for tool command [python '/tmp/tmptoruqmiy/galaxy-dev/tools/data_source/upload.py' '/tmp/tmptoruqmiy/galaxy-dev' '/tmp/tmptoruqmiy/job_working_directory/000/1/registry.xml' '/tmp/upload_params_7yd43mro' '1:/tmp/tmptoruqmiy/job_working_directory/000/1/working/dataset_97392d40-4be1-455b-b5a1-d46e4721e0d8_files:/tmp/tmptoruqmiy/files/9/7/3/dataset_97392d40-4be1-455b-b5a1-d46e4721e0d8.dat'] -2022-05-27 09:06:05,465 INFO [galaxy.tools] Validated and populated state for tool request (29.005 ms) -2022-05-27 09:06:05,474 DEBUG [galaxy.tools.actions.upload] Persisted uploads (0.156 ms) -2022-05-27 09:06:05,608 DEBUG [galaxy.tools.actions.upload] Checked uploads (133.631 ms) -2022-05-27 09:06:05,614 DEBUG [galaxy.tools.actions.upload] Created upload job (5.702 ms) -2022-05-27 09:06:05,635 INFO [galaxy.web_stack.handlers] (Job[id=2,tool_id=upload1]) Handler '_default_' assigned using 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method -2022-05-27 09:06:06,681 INFO [galaxy.jobs.handler] (2) Job dispatched -2022-05-27 09:06:06,896 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmptoruqmiy/job_working_directory/000/2/tool_script.sh] for tool command [python '/tmp/tmptoruqmiy/galaxy-dev/tools/data_source/upload.py' '/tmp/tmptoruqmiy/galaxy-dev' '/tmp/tmptoruqmiy/job_working_directory/000/2/registry.xml' '/tmp/upload_params_niqt66u4' '2:/tmp/tmptoruqmiy/job_working_directory/000/2/working/dataset_cb889cdf-730a-428f-b94b-82c19b5bb4f4_files:/tmp/tmptoruqmiy/files/c/b/8/dataset_cb889cdf-730a-428f-b94b-82c19b5bb4f4.dat'] -2022-05-27 09:06:13,887 INFO [galaxy.tools] Validated and populated state for tool request (21.823 ms) -2022-05-27 09:06:13,893 DEBUG [galaxy.tools.actions.upload] Persisted uploads (0.140 ms) -2022-05-27 09:06:14,001 DEBUG [galaxy.tools.actions.upload] Checked uploads (108.369 ms) -2022-05-27 09:06:14,007 DEBUG [galaxy.tools.actions.upload] Created upload job (5.655 ms) -2022-05-27 09:06:14,035 INFO [galaxy.web_stack.handlers] (Job[id=3,tool_id=upload1]) Handler '_default_' assigned using 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method -2022-05-27 09:06:14,310 INFO [galaxy.jobs.handler] (3) Job dispatched -2022-05-27 09:06:14,453 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmptoruqmiy/job_working_directory/000/3/tool_script.sh] for tool command [python '/tmp/tmptoruqmiy/galaxy-dev/tools/data_source/upload.py' '/tmp/tmptoruqmiy/galaxy-dev' '/tmp/tmptoruqmiy/job_working_directory/000/3/registry.xml' '/tmp/upload_params_4_iqbmvk' '3:/tmp/tmptoruqmiy/job_working_directory/000/3/working/dataset_30dd8d24-f614-4ac7-8cd6-a4e18b4f1f3e_files:/tmp/tmptoruqmiy/files/3/0/d/dataset_30dd8d24-f614-4ac7-8cd6-a4e18b4f1f3e.dat'] -2022-05-27 09:06:21,302 INFO [galaxy.tools] Validated and populated state for tool request (28.288 ms) -2022-05-27 09:06:21,362 INFO [galaxy.tools.actions] Handled output named sort_file for tool testtoolshed.g2.bx.psu.edu/repos/agpetit/concatenate_table/concatenate_table/1.0.0 (3.760 ms) -2022-05-27 09:06:21,377 INFO [galaxy.tools.actions] Added output datasets to history (14.220 ms) -2022-05-27 09:06:21,379 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=testtoolshed.g2.bx.psu.edu/repos/agpetit/concatenate_table/concatenate_table/1.0.0] complete, ready to be enqueued (1.770 ms) -2022-05-27 09:06:21,418 INFO [galaxy.web_stack.handlers] (Job[id=4,tool_id=testtoolshed.g2.bx.psu.edu/repos/agpetit/concatenate_table/concatenate_table/1.0.0]) Handler '_default_' assigned using 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method -2022-05-27 09:06:21,724 INFO [galaxy.jobs.handler] (4) Job dispatched -2022-05-27 09:06:22,041 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmptoruqmiy/job_working_directory/000/4/tool_script.sh] for tool command [cat /tmp/tmptoruqmiy/files/9/7/3/dataset_97392d40-4be1-455b-b5a1-d46e4721e0d8.dat | awk -F'\t' 'BEGIN{mean="Time (ps)"; std=""} /^Time/ {for (i=2; i<(NF+1); i++) gsub(" ", ",mean ",$i) ; for (i=2; i<(NF+1); i++) mean=mean "\t" $i ; for (i=2; i<(NF+1); i++) gsub(",mean", ",std ",$i); for (i=2; i<(NF+1); i++) std=std "\t" $i } END{print (mean std)}' &>> '/tmp/tmptoruqmiy/files/e/e/c/dataset_eec2e4de-bddf-4d25-b9b2-aa655cfec902.dat' ; cat /tmp/tmptoruqmiy/files/9/7/3/dataset_97392d40-4be1-455b-b5a1-d46e4721e0d8.dat | awk -F'\t' -v min=200.0 'BEGIN{min_val=min ; max_val=0 ; means=""; std=""} /^[0-9]/ {if ($1 <= min_val) {min_val=$1} ; if ($1 >= max_val) {max_val=$1}} ; /Mean/ {for (i=2; i<NF; i++) means=means"\t"$i ;means=means"\t"$NF } ; /Std/ {for (i=2; i<NF; i++) std=std"\t"$i; ;std=std"\t"$NF} END {print (min_val "-" max_val means std)}' &>> 'test.tabular' ; cat /tmp/tmptoruqmiy/files/c/b/8/dataset_cb889cdf-730a-428f-b94b-82c19b5bb4f4.dat | awk -F'\t' -v min=500.0 'BEGIN{min_val=min ; max_val=0 ; means=""; std=""} /^[0-9]/ {if ($1 <= min_val) {min_val=$1} ; if ($1 >= max_val) {max_val=$1}} ; /Mean/ {for (i=2; i<NF; i++) means=means"\t"$i ;means=means"\t"$NF } ; /Std/ {for (i=2; i<NF; i++) std=std"\t"$i; ;std=std"\t"$NF} END {print (min_val "-" max_val means std)}' &>> 'test.tabular' ; cat /tmp/tmptoruqmiy/files/3/0/d/dataset_30dd8d24-f614-4ac7-8cd6-a4e18b4f1f3e.dat | awk -F'\t' -v min=1000.0 'BEGIN{min_val=min ; max_val=0 ; means=""; std=""} /^[0-9]/ {if ($1 <= min_val) {min_val=$1} ; if ($1 >= max_val) {max_val=$1}} ; /Mean/ {for (i=2; i<NF; i++) means=means"\t"$i ;means=means"\t"$NF } ; /Std/ {for (i=2; i<NF; i++) std=std"\t"$i; ;std=std"\t"$NF} END {print (min_val "-" max_val means std)}' &>> 'test.tabular' ; cat 'test.tabular' | sort -k1 -n &>> '/tmp/tmptoruqmiy/files/e/e/c/dataset_eec2e4de-bddf-4d25-b9b2-aa655cfec902.dat'] - -------------------------------Captured log call-------------------------------- DEBUG multipart.multipart:multipart.py:604 Calling on_field_start with no data -DEBUG multipart.multipart:multipart.py:601 Calling on_field_name with data[0:4] -DEBUG multipart.multipart:multipart.py:601 Calling on_field_data with data[5:129] -DEBUG multipart.multipart:multipart.py:604 Calling on_field_end with no data -DEBUG multipart.multipart:multipart.py:604 Calling on_end with no data | |||
| Passed | -test/functional/test_toolbox_pytest.py::test_tool[testtoolshed.g2.bx.psu.edu/repos/agpetit/estimate_cut_sub_trajectories/estimate_cut_sub_trajectories/0.1.0_test_1] | -16.85 | -|
|
- ------------------------------Captured stderr call------------------------------ 2022-05-27 09:06:27,235 DEBUG [multipart.multipart] Calling on_field_start with no data -2022-05-27 09:06:27,236 DEBUG [multipart.multipart] Calling on_field_name with data[0:4] -2022-05-27 09:06:27,236 DEBUG [multipart.multipart] Calling on_field_data with data[5:153] -2022-05-27 09:06:27,237 DEBUG [multipart.multipart] Calling on_field_end with no data -2022-05-27 09:06:27,237 DEBUG [multipart.multipart] Calling on_end with no data -2022-05-27 09:06:27,445 INFO [galaxy.tools] Validated and populated state for tool request (22.082 ms) -2022-05-27 09:06:27,453 DEBUG [galaxy.tools.actions.upload] Persisted uploads (0.154 ms) -2022-05-27 09:06:27,567 DEBUG [galaxy.tools.actions.upload] Checked uploads (113.879 ms) -2022-05-27 09:06:27,572 DEBUG [galaxy.tools.actions.upload] Created upload job (5.676 ms) -2022-05-27 09:06:27,592 INFO [galaxy.web_stack.handlers] (Job[id=5,tool_id=upload1]) Handler '_default_' assigned using 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method -2022-05-27 09:06:28,223 INFO [galaxy.jobs.handler] (5) Job dispatched -2022-05-27 09:06:28,370 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmptoruqmiy/job_working_directory/000/5/tool_script.sh] for tool command [python '/tmp/tmptoruqmiy/galaxy-dev/tools/data_source/upload.py' '/tmp/tmptoruqmiy/galaxy-dev' '/tmp/tmptoruqmiy/job_working_directory/000/5/registry.xml' '/tmp/upload_params_3z8ry2g5' '5:/tmp/tmptoruqmiy/job_working_directory/000/5/working/dataset_fedb0d1a-a7bd-401b-86ba-117e6751df12_files:/tmp/tmptoruqmiy/files/f/e/d/dataset_fedb0d1a-a7bd-401b-86ba-117e6751df12.dat'] -2022-05-27 09:06:37,473 INFO [galaxy.tools] Validated and populated state for tool request (22.142 ms) -2022-05-27 09:06:37,488 INFO [galaxy.tools.actions] Handled output named sub_trajectories_out_file for tool testtoolshed.g2.bx.psu.edu/repos/agpetit/estimate_cut_sub_trajectories/estimate_cut_sub_trajectories/0.1.0 (2.549 ms) -2022-05-27 09:06:37,490 INFO [galaxy.tools.actions] Handled output named estimate_log for tool testtoolshed.g2.bx.psu.edu/repos/agpetit/estimate_cut_sub_trajectories/estimate_cut_sub_trajectories/0.1.0 (1.954 ms) -2022-05-27 09:06:37,505 INFO [galaxy.tools.actions] Added output datasets to history (15.426 ms) -2022-05-27 09:06:37,508 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=testtoolshed.g2.bx.psu.edu/repos/agpetit/estimate_cut_sub_trajectories/estimate_cut_sub_trajectories/0.1.0] complete, ready to be enqueued (2.166 ms) -2022-05-27 09:06:37,543 INFO [galaxy.web_stack.handlers] (Job[id=6,tool_id=testtoolshed.g2.bx.psu.edu/repos/agpetit/estimate_cut_sub_trajectories/estimate_cut_sub_trajectories/0.1.0]) Handler '_default_' assigned using 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method -2022-05-27 09:06:37,847 INFO [galaxy.jobs.handler] (6) Job dispatched -2022-05-27 09:06:37,982 WARNI [galaxy.security.object_wrapper] Unable to create dynamic subclass SafeStringWrapper(galaxy.model.none_like.None:<class 'NoneType'>,<class 'NotImplementedType'>,<class 'bool'>,<class 'bytearray'>,<class 'ellipsis'>,<class 'galaxy.security.object_wrapper.SafeStringWrapper'>,<class 'galaxy.tools.wrappers.ToolParameterValueWrapper'>,<class 'numbers.Number'>) for <class 'galaxy.model.none_like.NoneDataset'>, None: type() doesn't support MRO entry resolution; use types.new_class() -2022-05-27 09:06:38,056 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmptoruqmiy/job_working_directory/000/6/tool_script.sh] for tool command [[ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/aepetit/miniconda3/bin/activate' '/home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/aepetit/miniconda3/bin/activate' '/home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/aepetit/miniconda3/bin/activate' '/home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; ln -s '/tmp/tmptoruqmiy/files/f/e/d/dataset_fedb0d1a-a7bd-401b-86ba-117e6751df12.dat' 'PIP2.1_test_check.txt' && ln -s '/tmp/tmptoruqmiy/files/5/8/a/dataset_58ab194a-5436-4b35-aea0-6b66530a0562.dat' 'estimated_number_of_sub_trajectories.tsv' && python '/tmp/tmptoruqmiy/shed_tools/testtoolshed.g2.bx.psu.edu/repos/agpetit/estimate_cut_sub_trajectories/c09cf8acc4de/estimate_cut_sub_trajectories/estimate_cut_sub_trajectories.py' --input_check 'PIP2.1_test_check.txt' --verbose --output_file 'estimated_number_of_sub_trajectories.tsv' --log_output 'log/estimated_number_of_sub_trajectories.log' --nb_frames '3' --start_traj '' --end_traj ''] - -------------------------------Captured log call-------------------------------- DEBUG multipart.multipart:multipart.py:604 Calling on_field_start with no data -DEBUG multipart.multipart:multipart.py:601 Calling on_field_name with data[0:4] -DEBUG multipart.multipart:multipart.py:601 Calling on_field_data with data[5:153] -DEBUG multipart.multipart:multipart.py:604 Calling on_field_end with no data -DEBUG multipart.multipart:multipart.py:604 Calling on_end with no data | |||
| Passed | -test/functional/test_toolbox_pytest.py::test_tool[testtoolshed.g2.bx.psu.edu/repos/agpetit/visualize_pore_diameter_aqp/visualize_pore_diameter_aqp/0.1.0_test_1] | -23.96 | -|
|
- ------------------------------Captured stderr call------------------------------ 2022-05-27 09:08:03,555 DEBUG [multipart.multipart] Calling on_field_start with no data -2022-05-27 09:08:03,556 DEBUG [multipart.multipart] Calling on_field_name with data[0:4] -2022-05-27 09:08:03,556 DEBUG [multipart.multipart] Calling on_field_data with data[5:149] -2022-05-27 09:08:03,557 DEBUG [multipart.multipart] Calling on_field_end with no data -2022-05-27 09:08:03,557 DEBUG [multipart.multipart] Calling on_end with no data -2022-05-27 09:08:03,766 INFO [galaxy.tools] Validated and populated state for tool request (22.328 ms) -2022-05-27 09:08:03,772 DEBUG [galaxy.tools.actions.upload] Persisted uploads (0.146 ms) -2022-05-27 09:08:03,874 DEBUG [galaxy.tools.actions.upload] Checked uploads (101.847 ms) -2022-05-27 09:08:03,880 DEBUG [galaxy.tools.actions.upload] Created upload job (5.943 ms) -2022-05-27 09:08:03,908 INFO [galaxy.web_stack.handlers] (Job[id=15,tool_id=upload1]) Handler '_default_' assigned using 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method -2022-05-27 09:08:04,251 INFO [galaxy.jobs.handler] (15) Job dispatched -2022-05-27 09:08:04,484 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmptoruqmiy/job_working_directory/000/15/tool_script.sh] for tool command [python '/tmp/tmptoruqmiy/galaxy-dev/tools/data_source/upload.py' '/tmp/tmptoruqmiy/galaxy-dev' '/tmp/tmptoruqmiy/job_working_directory/000/15/registry.xml' '/tmp/upload_params_fom2zjay' '22:/tmp/tmptoruqmiy/job_working_directory/000/15/working/dataset_14d25761-af75-46cc-b88e-fff28f41b237_files:/tmp/tmptoruqmiy/files/1/4/d/dataset_14d25761-af75-46cc-b88e-fff28f41b237.dat'] -2022-05-27 09:08:11,110 INFO [galaxy.tools] Validated and populated state for tool request (11.546 ms) -2022-05-27 09:08:11,124 INFO [galaxy.tools.actions] Handled output named out_file for tool testtoolshed.g2.bx.psu.edu/repos/agpetit/visualize_pore_diameter_aqp/visualize_pore_diameter_aqp/0.1.0 (2.658 ms) -2022-05-27 09:08:11,126 INFO [galaxy.tools.actions] Handled output named out_file2 for tool testtoolshed.g2.bx.psu.edu/repos/agpetit/visualize_pore_diameter_aqp/visualize_pore_diameter_aqp/0.1.0 (1.971 ms) -2022-05-27 09:08:11,128 INFO [galaxy.tools.actions] Handled output named out_file3 for tool testtoolshed.g2.bx.psu.edu/repos/agpetit/visualize_pore_diameter_aqp/visualize_pore_diameter_aqp/0.1.0 (1.959 ms) -2022-05-27 09:08:11,131 INFO [galaxy.tools.actions] Handled output named out_file4 for tool testtoolshed.g2.bx.psu.edu/repos/agpetit/visualize_pore_diameter_aqp/visualize_pore_diameter_aqp/0.1.0 (2.792 ms) -2022-05-27 09:08:11,148 INFO [galaxy.tools.actions] Added output datasets to history (16.256 ms) -2022-05-27 09:08:11,150 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=testtoolshed.g2.bx.psu.edu/repos/agpetit/visualize_pore_diameter_aqp/visualize_pore_diameter_aqp/0.1.0] complete, ready to be enqueued (2.459 ms) -2022-05-27 09:08:11,183 INFO [galaxy.web_stack.handlers] (Job[id=16,tool_id=testtoolshed.g2.bx.psu.edu/repos/agpetit/visualize_pore_diameter_aqp/visualize_pore_diameter_aqp/0.1.0]) Handler '_default_' assigned using 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method -2022-05-27 09:08:11,681 INFO [galaxy.jobs.handler] (16) Job dispatched -2022-05-27 09:08:11,940 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmptoruqmiy/job_working_directory/000/16/tool_script.sh] for tool command [[ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/aepetit/miniconda3/envs/mulled-v1-5a4fbc211f26cb04dc98136056f4848655807f4df79e1bb9f5b172569688ee2f')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/aepetit/miniconda3/bin/activate' '/home/aepetit/miniconda3/envs/mulled-v1-5a4fbc211f26cb04dc98136056f4848655807f4df79e1bb9f5b172569688ee2f' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/aepetit/miniconda3/envs/mulled-v1-5a4fbc211f26cb04dc98136056f4848655807f4df79e1bb9f5b172569688ee2f')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/aepetit/miniconda3/bin/activate' '/home/aepetit/miniconda3/envs/mulled-v1-5a4fbc211f26cb04dc98136056f4848655807f4df79e1bb9f5b172569688ee2f' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/aepetit/miniconda3/envs/mulled-v1-5a4fbc211f26cb04dc98136056f4848655807f4df79e1bb9f5b172569688ee2f')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/aepetit/miniconda3/bin/activate' '/home/aepetit/miniconda3/envs/mulled-v1-5a4fbc211f26cb04dc98136056f4848655807f4df79e1bb9f5b172569688ee2f' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/aepetit/miniconda3/envs/mulled-v1-5a4fbc211f26cb04dc98136056f4848655807f4df79e1bb9f5b172569688ee2f')" ] || { -MAX_TRIES=3 -COUNT=0 -while [ $COUNT -lt $MAX_TRIES ]; do - . '/home/aepetit/miniconda3/bin/activate' '/home/aepetit/miniconda3/envs/mulled-v1-5a4fbc211f26cb04dc98136056f4848655807f4df79e1bb9f5b172569688ee2f' > conda_activate.log 2>&1 - if [ $? -eq 0 ];then - break - else - let COUNT=COUNT+1 - if [ $COUNT -eq $MAX_TRIES ];then - echo "Failed to activate conda environment! Error was:" - cat conda_activate.log - exit 1 - fi - sleep 10s - fi -done -} ; ln -s '/tmp/tmptoruqmiy/files/1/4/d/dataset_14d25761-af75-46cc-b88e-fff28f41b237.dat' 'table_sort_pore_diameter_aqp.tabular' && Rscript '/tmp/tmptoruqmiy/shed_tools/testtoolshed.g2.bx.psu.edu/repos/agpetit/visualize_pore_diameter_aqp/3cdcc6eeb3ec/visualize_pore_diameter_aqp/visualize_pore_diameter_aqp.R' -i 'table_sort_pore_diameter_aqp.tabular' -a TRUE -p TRUE -d TRUE -f TRUE] -2022-05-27 09:08:24,745 INFO [galaxy.tool_util.verify] ## files diff on '/tmp/tmpher3091iall_graphics_distribution.pdf' and '/tmp/tmpc_uqkw8kall_graphics_distribution.pdf': lines_diff = 0, found diff = 4, found pdf invalid diff = 0 - -------------------------------Captured log call-------------------------------- DEBUG multipart.multipart:multipart.py:604 Calling on_field_start with no data -DEBUG multipart.multipart:multipart.py:601 Calling on_field_name with data[0:4] -DEBUG multipart.multipart:multipart.py:601 Calling on_field_data with data[5:149] -DEBUG multipart.multipart:multipart.py:604 Calling on_field_end with no data -DEBUG multipart.multipart:multipart.py:604 Calling on_end with no data ----------------------------Captured stderr teardown---------------------------- 2022-05-27 09:08:24,841 INFO [test_driver] 21 threads were active before stopping embedded server -2022-05-27 09:08:24,841 INFO [test_driver] Shutting down embedded galaxy uvicorn server -2022-05-27 09:08:24,841 INFO [test_driver] Embedded web server galaxy stopped -2022-05-27 09:08:24,841 INFO [test_driver] Stopping embedded server thread -INFO: Shutting down -2022-05-27 09:08:24,911 INFO [uvicorn.error] Shutting down -INFO: Waiting for application shutdown. -2022-05-27 09:08:25,013 INFO [uvicorn.error] Waiting for application shutdown. -INFO: Application shutdown complete. -2022-05-27 09:08:25,013 INFO [uvicorn.error] Application shutdown complete. -INFO: Finished server process [23683] -2022-05-27 09:08:25,014 INFO [uvicorn.error] Finished server process [23683] -2022-05-27 09:08:25,015 INFO [test_driver] Event loop for uvicorn closed -2022-05-27 09:08:25,016 INFO [test_driver] Embedded server thread stopped -2022-05-27 09:08:25,016 INFO [test_driver] Stopping application galaxy -2022-05-27 09:08:26,298 INFO [galaxy.queue_worker] Sending reconfigure_watcher control task. -2022-05-27 09:08:26,325 INFO [galaxy.jobs.handler] sending stop signal to worker thread -2022-05-27 09:08:27,337 INFO [galaxy.jobs.handler] job handler queue stopped -2022-05-27 09:08:27,338 INFO [galaxy.jobs.runners] LocalRunner: Sending stop signal to 4 job worker threads -2022-05-27 09:08:27,338 INFO [galaxy.jobs.runners] Waiting up to 5 seconds for job worker threads to shutdown... -2022-05-27 09:08:27,339 INFO [galaxy.jobs.runners] All job worker threads shutdown cleanly -2022-05-27 09:08:27,340 INFO [galaxy.jobs.runners] TaskRunner: Sending stop signal to 2 job worker threads -2022-05-27 09:08:27,340 INFO [galaxy.jobs.runners] Waiting up to 5 seconds for job worker threads to shutdown... -2022-05-27 09:08:27,468 INFO [galaxy.jobs.runners] All job worker threads shutdown cleanly -2022-05-27 09:08:27,469 INFO [galaxy.jobs.handler] sending stop signal to worker thread -2022-05-27 09:08:27,469 INFO [galaxy.jobs.handler] job handler stop queue stopped -2022-05-27 09:08:27,470 INFO [test_driver] Application galaxy stopped. -2022-05-27 09:08:27,471 INFO [test_driver] 2 active after stopping embedded server - -----------------------------Captured log teardown------------------------------ INFO test_driver:driver_util.py:747 21 threads were active before stopping embedded server -INFO test_driver:driver_util.py:755 Shutting down embedded galaxy uvicorn server -INFO test_driver:driver_util.py:757 Embedded web server galaxy stopped -INFO test_driver:driver_util.py:760 Stopping embedded server thread -INFO uvicorn.error:server.py:252 Shutting down -INFO uvicorn.error:on.py:64 Waiting for application shutdown. -INFO uvicorn.error:on.py:75 Application shutdown complete. -INFO uvicorn.error:server.py:85 Finished server process [23683] -INFO test_driver:driver_util.py:587 Event loop for uvicorn closed -INFO test_driver:driver_util.py:762 Embedded server thread stopped -INFO test_driver:driver_util.py:765 Stopping application galaxy -INFO test_driver:driver_util.py:767 Application galaxy stopped. -INFO test_driver:driver_util.py:769 2 active after stopping embedded server | |||